[gmx-users] how to make index of a micelle

[Justin Lemkul]

On 11/18/19 12:13 PM, Giuseppe R Del Sorbo wrote:
> Dear Justin,
>
> I want to make an index for the micelle, made od 60 molecules of SDS.
>

So, if I understand correctly, the SDS micelle does not contain all of 
the SDS molecules in the system? That was not clear in your original 
email. If that's the case, the only option is to specify the residue 
numbers individually or to use gmx select with a geometric criterion for 
the spatial coordinates that the micelle occupies. See "gmx help 
selections" for examples.

-Justin

> Thanks for the email.
>
> Best,
>
> Giuseppe
>
>
> Il 2019-11-18 18:09 Justin Lemkul ha scritto:
>> On 11/18/19 11:43 AM, Giuseppe R Del Sorbo wrote:
>>> Dear all,
>>>
>>> In my simulation I have a lysine + micelle of SDS.
>>>
>>> In the analysis, I want to find the spherical radial distribution 
>>> functions of methyl groups around the center of mass of the micelle.
>>>
>>> I Know how to make the index for the methyl group, but how can I 
>>> make an index for the micelle?
>>>
>>
>> The SDS molecules should already be a default group in the list of
>> available selections. You shouldn't even need a custom group for it.
>>
>> -Justin
>>
>> -- 
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================